but I have the torsion angles , bond angles for my residue .. The problem is I don't know which one to put where as the charmm FF parameter that I have got doesnot match with the charmm ff parameter in gromacs.. that's y I am confused ..<br>
<br><div class="gmail_quote">On Thu, Mar 3, 2011 at 12:58 AM, Jianguo Li <span dir="ltr"><<a href="mailto:ljggmx@yahoo.com.sg">ljggmx@yahoo.com.sg</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div><div style="font-family:times new roman,new york,times,serif;font-size:12pt">My way of doing it is:<br><div style="font-family:times new roman,new york,times,serif;font-size:12pt">(1) add two new residues entries (with two different names) for glycine and seine in the rtp file and corresponding FF files. The new entries in the rtp file for glycine and serine should have
the same number of atoms as in the real molecule (delete the unnecessary H
or OH groups if needed)<br>(2) then use pdb2gmx <br>(3) then manually construct the bond, angle and dihedrals at the linkage site. <br><br>Cheers,<br>Jianguo<br><br><div style="font-family:times new roman,new york,times,serif;font-size:12pt">
<font size="2" face="Tahoma"><hr size="1"><b><span style="font-weight:bold">From:</span></b> bharat gupta <<a href="mailto:bharat.85.monu@gmail.com" target="_blank">bharat.85.monu@gmail.com</a>><br><b><span style="font-weight:bold">To:</span></b> Discussion list for GROMACS users <<a href="mailto:gmx-users@gromacs.org" target="_blank">gmx-users@gromacs.org</a>><br>
<b><span style="font-weight:bold">Sent:</span></b> Thursday, 3 March 2011 11:31:38<br><b><span style="font-weight:bold">Subject:</span></b> [gmx-users] Re: adding ff parameter of modified residue to charmm ff<br></font><div>
<div></div><div class="h5"><br>Hi,<div><br></div><div>I followed the tutorial - <span style="border-collapse:collapse;font-family:arial,sans-serif;font-size:13px"><a rel="nofollow" href="http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field" style="color:rgb(0, 0, 204)" target="_blank">http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field</a> for updating the Charmm FF for my modified residue ..</span></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">I added the residues to the .rtp file , then I added the new atom types in .atp file , </span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">The compound has some linkage with serine and glycine ... I want to know how and where shall I add the linkage parameters and the parameters (in bits) given below</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br></span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse"><br>
</span></font></div><div><font face="arial, sans-serif"><span style="border-collapse:collapse">(The parameter file of the compound looks like this ) ..</span></font></div>
<div><font face="arial, sans-serif"><span style="border-collapse:collapse"> </span></font></div><div><font face="arial, sans-serif"><div style="border-collapse:collapse">
BONDS</div><div style="border-collapse:collapse">!</div><div style="border-collapse:collapse">!V(bond) = Kb(b - b0)**2</div><div style="border-collapse:collapse">!</div><div style="border-collapse:collapse">!Kb: kcal/mole/A**2</div>
<div style="border-collapse:collapse">!b0: A</div><div style="border-collapse:collapse">!</div><div style="border-collapse:collapse">!atom type Kb b0</div><div style="border-collapse:collapse">CA1 CA2 305.00 1.3750 !</div>
<div style="border-collapse:collapse">CA2 CA3 305.00 1.3750 !</div><div style="border-collapse:collapse">CA3 CA4 305.00 1.3750 !</div><div style="border-collapse:collapse">HPc CA1 340.000 1.08 !</div>
<div style="border-collapse:collapse">HPc CA2 340.000 1.08 !</div><div style="border-collapse:collapse">HPc CA3 340.000 1.08 !</div><div style="border-collapse:collapse">HPc CA4 340.000 1.08 !</div>
<div style="border-collapse:collapse"><br></div><div style="border-collapse:collapse"><br></div><div style="border-collapse:collapse"><div>ANGLES</div><div>!</div><div>!V(angle) = Ktheta(Theta - Theta0)**2</div><div>
!</div><div>!V(Urey-Bradley) = Kub(S - S0)**2</div><div>!</div><div>!Ktheta: kcal/mole/rad**2</div><div>!Theta0: degrees</div><div>!Kub: kcal/mole/A**2 (Urey-Bradley)</div><div>!S0: A</div><div>!</div><div>!atom types Ktheta Theta0 Kub S0</div>
<div>!</div><div>NR2c CP2c NR1c 130.00 114.00 ! </div><div>CP2c NR2c CP1c 130.00 106.00 ! </div><div>CP2c NR1c CP1c 130.00 107.90 ! </div><div>NR2c CP1c CP1c 130.00 108.30 ! </div><div>NR2c CP1c CE1c 45.80 129.50 ! </div>
<div>NR1c CP1c OcH 42.00 126.00 !</div><div>NR1c CP1c CP1c 130.00 103.00 ! </div></div><div style="border-collapse:collapse"><br></div><div style="border-collapse:collapse"><br></div><div style="border-collapse:collapse">
<div>!Connection to the ser fragment</div><div>!------------------------------</div><div>CT2 CT1 CP2c 52.000 108.0000 ! ALLOW ALI PEP POL ARO</div><div>HB CT1 CP2c 50.000 109.5000 ! ALLOW PEP</div><div>NH1 CT1 CP2c 50.000 107.0000 ! ALLOW PEP POL ARO ALI</div>
<div>NR2C CP2C CT1 40.00 125.00 ! </div></div><div style="border-collapse:collapse"><br></div><div style="border-collapse:collapse"><br></div><div style="border-collapse:collapse"><br></div><div style="border-collapse:collapse">
<div>!Connection to the gly fragment</div><div>!------------------------------</div><div>NR1C CT2 C 50.000 107.0000 </div><div>NR1c CT2 HB 48.000 108.0000</div><div>CP2C NR1C CT2 36.00 129.00</div><div>
CP1C NR1C CT2 32.00 123.40</div><div>!</div><div>DIHEDRALS</div><div>!</div><div>!V(dihedral) = Kchi(1 + cos(n(chi) - delta))</div><div>!</div><div>!Kchi: kcal/mole</div><div>!n: multiplicity</div><div>!delta: degrees</div>
<div>!</div><div>!atom types Kchi n delta</div><div>!</div><div>CP2C NR2C CP1C CP1C 14.0000 2 180.00 ! </div><div>CP2C NR1C CP1C CP1C 14.0000 2 180.00 !</div><div>NR2C CP2C NR1C CP1C 14.0000 2 180.00 !</div>
<div>NR2C CP1C CP1C NR1C 4.0000 2 180.00 ! </div><div>NR1C CP2C NR2C CP1C 4.0000 2 180.00 ! </div><div>CA1 CA2 CA3 CA4 3.1000 2 180.00 ! </div></div><div style="border-collapse:collapse"><br></div>
<div style="border-collapse:collapse"><br></div><div style="border-collapse:collapse"><div>!barrier CA-CB</div><div>CP1C CP1C CE1C HA1C 6.84 2 180.00 ! </div><div>CP1C CP1C CE1C CA1 6.84 2 180.00 !</div>
<div>NR2C CP1C CE1C HA1C 6.84 2 180.00 !</div><div>NR2C CP1C CE1C CA1 6.84 2 180.00 ! </div><div>!</div><div>!barrier CB-CG2</div><div>CP1C CE1C CA1 CA2 1.4 2 180.00 ! </div><div>HA1C CE1C CA1 CA2 1.4 2 180.00 ! </div>
<div>!</div><div>CP2C NR1C CP1C OCH 14.00 2 180.00 !</div><div>NR2C CP2C NR1C CT2 14.00 2 180.00 !</div><div>NR2C CP1C CP1C OCH 14.00 2 180.00 !</div><div>CP1C NR1C CP2C CT1 14.00 2 180.00 !</div>
<div>OCH CP1C NR1C CT2 14.00 2 180.00 !</div><div>CP1C NR2C CP2C CT1 14.00 2 180.00 !</div><div>CP1C CP1C NR1C CT2 14.00 2 180.00 !</div><div>CT1 CP2C NR1C CT2 14.00 2 180.00 !</div>
<div>!</div><div>! Linking the chromophore and the glycine fragment</div><div>O C CT2 NR1C 0.0000 1 0.00 ! </div><div>NH1 C CT2 NR1c 0.6000 1 0.00 ! </div><div>CP2C NR1C CT2 HB 0.032 3 0.00 ! </div>
<div>CP2c NR1c CT2 C 0.032 3 0.00 !</div><div>CP1c NR1c CT2 HB 0.032 3 180.00 !</div><div>CP1c NR1c CT2 C 0.032 3 180.00 !</div><div>!</div><div>! Linking the chromophore and the serine fragment</div>
<div>C NH1 CT1 CP2C 0.2000 1 180.00 !</div><div>H NH1 CT1 CP2C 0.0000 1 0.00 !</div><div>NR2C CP2C CT1 HB 0.105 3 180.00 ! </div><div>NR2C CP2C CT1 NH1 0.105 3 180.00 ! </div>
<div>NR2C CP2C CT1 CT2 0.105 3 180.00 ! </div><div>NR1C CP2C CT1 HB 0.105 3 0.00 ! </div></div><div style="border-collapse:collapse"><br></div><div style="border-collapse:collapse"><br></div>
<div style="border-collapse:collapse"><div>IMPROPER</div><div>!</div><div>!V(improper) = Kpsi(psi - psi0)**2</div><div>!</div><div>!Kpsi: kcal/mole/rad**2</div><div>!psi0: degrees</div><div>!note that the second column of numbers (0) is ignored</div>
<div>!</div><div>!atom types Kpsi psi0</div><div>!</div><div>CP2C NR2C NR1C CT1 0.5 0 0.00</div><div>CP2C NR1C NR2C CT1 0.5 0 0.00</div><div>!</div><div>
CP1C NR1C CP1C OCH 0.5 0 0.00</div><div>CP1C CP1C NR1C OCH 0.5 0 0.00</div><div>!</div><div>NR1C CP1C CP2C CT2 0.45 0 0.00 </div><div>NR1C CP2C CP1C CT2 0.45 0 0.00 </div>
<div>!</div><div>CP1C NR2C CP1C CE1C 220.0 0 0.00</div><div>CP1C CP1C NR2C CE1C 220.0 0 0.00</div></div><div style="border-collapse:collapse"><br></div><div style="border-collapse:collapse">
<br></div><div><div><span style="border-collapse:collapse">!</span></div><div><span style="border-collapse:collapse">!V(Lennard-Jones) = Eps,i,j[(Rmin,i,j/ri,j)**12 - 2(Rmin,i,j/ri,j)**6]</span></div>
<div><span style="border-collapse:collapse">!</span></div><div><span style="border-collapse:collapse">!epsilon: kcal/mole, Eps,i,j = sqrt(eps,i * eps,j)</span></div><div>
<span style="border-collapse:collapse">!Rmin/2: A, Rmin,i,j = Rmin/2,i + Rmin/2,j</span></div><div><span style="border-collapse:collapse">!</span></div><div><span style="border-collapse:collapse">!atom ignored epsilon Rmin/2 ignored eps,1-4 Rmin/2,1-4</span></div>
<div><span style="border-collapse:collapse">!</span></div><div><span style="border-collapse:collapse">!CAc 5.000000 -0.070000 1.992400 ! ALLOW ARO</span></div>
<div><span style="border-collapse:collapse">! ! benzene (JES)</span></div><div><span style="border-collapse:collapse">CA1 5.000000 -0.070000 1.992400 ! ALLOW ARO</span></div>
<div><span style="border-collapse:collapse">CA2 5.000000 -0.070000 1.992400 ! ALLOW ARO</span></div><div><span style="border-collapse:collapse">CA3 5.000000 -0.070000 1.992400 ! ALLOW ARO</span></div>
<div><span style="border-collapse:collapse">CA4 5.000000 -0.070000 1.992400 ! ALLOW ARO</span></div><div><span style="border-collapse:collapse">CE1c 0.000000 -0.068000 2.090000 ! </span></div>
<div><span style="border-collapse:collapse"><span style="white-space:pre-wrap"> </span>! for propene, yin/adm jr., 12/95</span></div><div><span style="border-collapse:collapse">CP1c 0.000000 -0.050000 1.800000 ! ALLOW ARO</span></div>
<div><span style="border-collapse:collapse"> ! adm jr., 10/23/91, imidazole solvation and sublimation</span></div><div><span style="border-collapse:collapse">CP2c 0.000000 -0.050000 1.800000 ! ALLOW ARO</span></div>
<div><span style="border-collapse:collapse"> ! adm jr., 10/23/91, imidazole solvation and sublimation</span></div><div><span style="border-collapse:collapse">CT3c 0.000000 -0.080000 2.060000 0.000000 -0.010000 1.900000 ! ALLOW ALI</span></div>
<div><span style="border-collapse:collapse"> ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92</span></div><div><span style="border-collapse:collapse">!</span></div>
<div><span style="border-collapse:collapse">Hch -2.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC</span></div><div><span style="border-collapse:collapse"> ! same as TIP3P hydrogen, adm jr., 7/20/89</span></div>
<div><span style="border-collapse:collapse">HAc 0.000000 -0.022000 1.320000 ! ALLOW PEP ALI POL SUL ARO PRO ALC</span></div><div><span style="border-collapse:collapse"> ! methane/ethane a.i. and ethane pure solvent, adm jr, 2/3/92</span></div>
<div><span style="border-collapse:collapse">HA1c 0.000000 -0.031000 1.250000 !</span></div><div><span style="border-collapse:collapse"> ! for propene, yin/adm jr., 12/95</span></div>
<div><span style="border-collapse:collapse">HPc 0.000000 -0.030000 1.358200 0.000000 -0.030000 1.358200 ! ALLOW ARO</span></div><div><span style="border-collapse:collapse"> ! JES 8/25/89 values from Jorgensen fit to hydration energy</span></div>
<div><span style="border-collapse:collapse">!</span></div><div><span style="border-collapse:collapse">NR1c 0.000000 -0.200000 1.850000 ! ALLOW ARO</span></div><div>
<span style="border-collapse:collapse"> ! His, adm jr., 9/4/89</span></div><div><span style="border-collapse:collapse">NR2c 0.000000 -0.200000 1.850000 ! ALLOW ARO</span></div>
<div><span style="border-collapse:collapse"> ! His, adm jr., 9/4/89</span></div><div><span style="border-collapse:collapse">!</span></div><div><span style="border-collapse:collapse">!Och 0.000000 -0.120000 1.700000 0.000000 -0.120000 1.400000 ! ALLOW PEP POL</span></div>
<div><span style="border-collapse:collapse">! ! This 1,4 vdW allows the C5 dipeptide minimum to exist.(LK)</span></div><div><span style="border-collapse:collapse">Och 0.000000 -0.120000 1.700000! ALLOW PEP POL, suppression du terme 1,4 (N.R. 10/2000)</span></div>
<div><span style="border-collapse:collapse">OHc 0.000000 -0.152100 1.770000 ! ALLOW ALC ARO</span></div><div><span style="border-collapse:collapse"> ! adm jr. 8/14/90, MeOH nonbond and solvent (same as TIP3P)</span></div>
<div><span style="border-collapse:collapse"><br></span></div><div><span style="border-collapse:collapse">HBOND CUTHB 0.5 ! If you want to do hbond analysis (only), then use</span></div>
<div><span style="border-collapse:collapse"> ! READ PARAM APPEND CARD</span></div><div><span style="border-collapse:collapse"> ! to append hbond parameters from the file: par_hbond.inp</span></div>
<div><span style="border-collapse:collapse"><br></span></div><div><span style="border-collapse:collapse">END</span></div></div><div style="border-collapse:collapse">
<br></div></font><br>-- <br>Bharat<br>Ph.D. Candidate<br>Room No. : 7202A, 2nd Floor<br>Biomolecular Engineering Laboratory<br>Division of Chemical Engineering and Polymer Science<br>Pusan National University<br>Busan -609735<br>
South Korea<br>Lab phone no. - +82-51-510-3680, +82-51-583-8343<div>Mobile no. - 010-5818-3680<br>E-mail : <a rel="nofollow" href="mailto:monu46010@yahoo.com" target="_blank">monu46010@yahoo.com</a></div><br>
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